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DNACLUST specifications

Information


Unique identifier OMICS_01955
Name DNACLUST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for DNACLUST

DNACLUST in publications

 (19)
PMCID: 5705604
PMID: 29184138
DOI: 10.1038/s41467-017-01982-7

[…] lengths were at least 50% the protein sequences, thereby confirming the new set of genes include most of the previous set., monomers in each chromosome of each strain separately were clustered using dnaclust. from each cluster with >10 monomers, the longest monomer was selected as the representative. to calculate the alignment between a pair of two representative monomers, the similarity […]

PMCID: 5601483
PMID: 28916791
DOI: 10.1038/s41598-017-11677-0

[…] identified from the isotig gene models. in total, 84 and 95 genes with splicing variants were identified for mt− and mt+, respectively (supplementary tables  and ). clustering analyses using the dnaclust package were performed for the genes in the hmts genomic regions in mt− and mt+; after manual correction of the clusters, they were classified into 46 and 67 clusters that were defined […]

PMCID: 5515451
PMID: 28719634
DOI: 10.1371/journal.pone.0181545

[…] below quality 20. filtered reads were clustered with the innovation centre clustering algorithm. briefly, reads were clustered at 100% identity and clustered/denoised at 99% identity using dnaclust (http://dnaclust.sourceforge.net/). clusters with an abundance below 3 were discarded. remaining clusters were scanned for chimeras with uchime denovo and uchime reference [] and clustered […]

PMCID: 5335695
PMID: 28253864
DOI: 10.1186/s12866-017-0947-0

[…] of 250 bp and paired-end assembled using flash software []. read counts per sample were checked to confirm no sample failed to be amplified or sequenced. reads were clustered at 97% identity using dnaclust [] and clusters showing abundances higher than 3 were then scanned for chimeras with uchime denovo and uchime reference in order to estimate final operational taxonomic units (otus) []. otus […]

PMCID: 5298331
PMID: 28178315
DOI: 10.1371/journal.pone.0171911

[…] (ccs) reads were obtained using pacbio smrtanalysis (version 2.2.0) software. after removal of low quality reads and scanning for chimeras, a total of 110,985 ccs were kept and clustered at 97% id (dnaclust version 3),which gave a total of 94,418 reads representing 44,919 clusters. representative sequence clusters were classified with the rdp classifier (version 2.5) [] with an in—house […]

DNACLUST institution(s)
Department of Computer Science, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, MD, USA
DNACLUST funding source(s)
This work was supported by the National Institutes of Health [R01-HG-004885]; the National Science Foundation [IIS-0812111]; and the Bill and Melinda Gates Foundation.

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